Current peer-reviewed journal
software does not meet the needs of NGOs and institutions in
developing countries. Olorien is a new software package to meet this
need. Olorien provides an automated system for article submission,
tracking, peer review, and publication. It publishes volumes online,
and creates print-ready PDF files automatically. To meet the needs of
NGOs and developing institutions, Olorien is free to use, and open
source. The system supports publication in almost any known language,
and is low cost to maintain. The architecture is built on open-source
components, and incorporates modern web standards. Olorien is
actively developed, and features continue to be added.

Background

The shift from paper to the
screen Traditionally, scientific journals have been paper-based
publications, released between quarterly and yearly. However, the
advent of the Internet has made much more rapid dissemination
possible. The Internet and the associated idea of Open Source have
also brought about more open access to research for the general
public. With this shift in how information is published and accessed,
a variety of tools have been developed to allow institutions to
leverage the Internet in their peer-reviewed journals. More than 15
applications for publishing are currently available.

Among these programs, a common
core of features has developed:
• Automated Submission: Allows
users to submit articles that are formatted and prepared for the
editorial staff without any work from the journal staff.
• Automated Notification: Keeps
all parties up to date on the progress of a submission, by email or
other means.
• Article Assignment and
Tracking: Allows tracking of a submitted article, assignment to peers
for review, and online review.
• copyediting: Allows the
editors to edit the article for better formatting without
resubmission.
• Automatic formatting and
online publishing of reviewed articles: Articles are automatically
formatted by the software to display correctly online, and can be
published on an external web site without work.
• Secure Access: Users must log
into the site to access articles and reviews. Certain functionality
is limited to the Editor-in-Chief.

Fee-based
access

There is some debate on fee-based
journals. Proponents point out that charging for access allows them
to fund and maintain a high-quality body of work. Opponents argue
that information should be free and open, and limiting research to a
select few who can afford access increases the social divide between
wealthy and poor. Free-information advocates also argue that
fee-based publications limit cross-disciplinary advances, and
ultimately, scientific progress. While both of these arguments have
merit, well-derived technology has the potential to make the debate
moot. If computer software can reduce the cost and labor of producing
a high-quality journal, fees can be greatly reduced, or outright
eliminated. Clearly this would be the best of both worlds. NGOs and
Developing Institutions Existing software can work well for
established institutions, but Non-Governmental Organizations (NGOs)
and institutions in developing countries have an additional set of
needs that are not currently addressed by existing applications.

• Multilingual publishing:
Journals should be able to be published in any known language.
• Low or No Cost licensing: The
software should be free, or have a low-cost option on its license.
• Low cost maintenance: The
software must be easy to use, and have low requirements for hardware
and time needed.
• Automatic creation of
print-ready publications: The software should create print-ready
files to reduce print preparation costs and time.

These needs are not addressed by
an existing software package. In many cases, organizations can get
caught in a downward spiral - lack of financial resources keeps them
from publishing, which limits their financial resources. The Olorien
project aims to reverse that spiral.

Olorien - a
peer-reviewed journal, for free

Olorien is a framework designed
to meet the needs of NGOs and institutions in developing countries.
It is a fully automated system for the creation of a peer-reviewed
journal for both print and web. Olorien natively supports publication
in any language, and it is completely free to use. Olorien was
developed to provide a journal for Lyon Arboretum at the University
of Hawai'i, and has been extended and opened for use by the general
public. Olorien was created by the company Quantum Imagery, and is
available for download at their site
http://www.quantumimagery.com/olorien. It is an actively maintained
and developed project, and will continue to add features in the years
and months ahead.

Framework
Features

First and foremost, Olorien is a
complete solution for management, peer review, and publication of a
Journal. It supports all of the core features common to online peer
review software, and also contains a few extra features of its own.

Publication
Cycle overview

Olorien follows a traditional
cycle for peer-reviewed publications, but allows the software to
replace some of the repetitive tasks. Figure 1 shows the flow from
submission to publication.

Automated
article submission

Olorien allows article
submissions from anyone who has signed up for a free account. To
submit an article, users go to "Submit an Article" page. On the
submission page, they first type in their article title, abstract,
and author attributions. Next, the user attaches the body text as
either a plain text or HTML file. For convenience, Olorien can
process the HTML generated by most popular word processors. Finally,
the user attaches all of the images, figures, and tables used in the
article. There is no limit to the number of full-color figures,
diagrams, photographs, and tables allowed.
Once submitted, Olorien
automatically manages the typesetting and formatting. To begin,
Olorien re-formats the submitted article to be consistent with the
look and feel of the journal, inserts any attached figures or images,
and translates any Olorien-specific markup used. From that "cleaned
up" document, the application then creates a formatted HTML page
for viewing online, and a print-ready PDF file for proofing. Both are
immediately available for access by the author, and editor-in-chief.
Once the typesetting is complete, an email is sent to the
editor-in-chief notifying them of the new submission.

Peer review
(Assignment and Tracking)

All new submissions are
immediately available to the editorial staff for assignment. Editors
can easily assign article to qualified reviewers for review,
comments, and recommendations. Olorien immediately emails the
reviewer(s) that they have a new article for review, and the
submitted article appears in the reviewer's Olorien inbox. The
reviewer can then download the article in PDF format or view it
online, then submit their review using the web site. Notification
then is sent back to the editors and editor-in-chief that a review is
in. This process can be repeated with several reviewers, and can run
in parallel, with several reviewers assigned to a given article
simultaneously. Finally, once the editors have enough information to
make a decision, the editor-in-chief submits the publication
decision, and the author is notified. If the article is accepted, it
is then assigned to a volume-in-progress in preparation for
publication.

Copyediting

In many cases, this generated PDF
is immediately suitable for print. In other cases, editors may prefer
to use the copyediting features to fine-tune placement of page
breaks, etc. In these cases, Olorien allows the Editor-in-Chief (EIC)
to edit the text of any submitted article, and to edit and re-upload
any images or diagrams. Since much of the copyediting emphasis is on
how the article will look in printed form, Olorien allows the
Editor-in-Chief to "regenerate" the PDF for edited articles and
volumes at any time.

Secure
access and user management

In traditional journal review
processes, there is a clear delineation between authors, reviewers,
and editors. In Olorien, we have used the same ideas in defining user
classes. Olorien supports five "classes" of users: the general
public, "normal" users (can submit manuscripts), reviewers,
editors, and editors-in-chief. Figure 1 shows the abilities of each
of these classes.

Figure 1: Olorien publication flow

The assignment of a user's
class is controlled completely by the editor-in-chief, using an
online interface.

Automated
notification

Whenever an important event
occurs, Olorien automatically notifies users via email and their
Olorien inbox. Currently, users are notified for the following
events:

To be a viable solution for
scientific journals, Olorien includes full volume management. The
editor-in-chief can create any number of volumes, and assign
submitted articles to any of these volumes. Since volume creation,
distribution, and archiving is an ongoing process, Olorien supports a
"life-cycle" of volume development. Volumes have a range of five
states into which they can be placed:

• In Progress, Private
• In Progress, Public
• Published
• Published, Featured Issue
• Archived

Each of these states changes the
way the volume is displayed on the public site, and who can view the
volume. The editor-in-chief can change the state of volumes at any
point, and articles can be edited and revised for typographic errors
throughout the process. However, once a volume is archived, neither
it nor its constituent articles can be changed.
Enhanced markup for web-specific
features one advantage of an Internet-based journal is that it can
take advantage of the unique capabilities offered by an HTML based
system over its print counterparts. In Olorien, we have developed a
simple markup set that authors can use to insert "tags" into
their documents for advanced features like automatic cross-reference
links, linked citation references and directly linked URLs for online
sources. A complete list of Olorien tags is available in the online
manual http://www.quantumimagery.com/olorien/manual. Authors simply
have to type the tags into their documents before upload, and Olorien
automatically processes and creates all the HTML and PDF code needed.
Olorien also has a list of tags for standard document elements, such
as section headers, subheadings and figures. Finally, for authors who
choose to write their articles in plain text, as is recommended,
there are also Olorien tags for most standard word-processor markup
like bold and italics.

Integrated
mailing list

To simplify deployment of a full
journal-focused web site, Olorien also includes a simple mailing list
manager. It allows members of the public to sign up for notifications
of new volumes. Messages can be sent to the list by the
editor-in-chief using a web-based interface. Notably, the email
interface includes pre-made templates that include the table of
contents for recently published issues, and direct links to the
articles. This allows the Editor-in-chief to efficiently publish and
promote a new volume. Figure 2 shows the email interface and the
resulting email message.

In a global research environment,
it is critical that publishing software supports languages outside
the Latin character set. Olorien is based on the UTF-8 subset of
Unicode. Using UTF-8, Olorien to supports article submission in
almost every language used in the world today. This includes over 650
languages, including German, Chinese, Russian, and less well-known
languages like Oromo and Dzongkha. The UTF-8 specification is
maintained by http://www.unicode.org/consortium/consort.html

TheUnicodeConsortium, and full
specifications are available at http://www.unicode.org
Because most modern computer
operating systems and word processors supportUTF-8, authors do not
have to make any changes to their systems to take advantage of this
functionality. A brief list of UTF-8 and Unicode-enabled products is
below.

Olorien also supports titles and
abstracts in two languages for all articles. This allows
organizations to publish the full article in its original language,
and provide an abstract and title in a common language, such as
English or Spanish. In future versions, Olorien will allow full
versions of an article in an arbitrary number of languages.

No Cost
Licensing

Olorien is completely free for
use by the general public. There is no charge to download, install,
or use the software in any environment. Since one of Olorien's key
goals is to provide a no-cost solution for publishing academic
research, there will never be a charge to use Olorien.
Users are free to use Olorien for
a journal that requires a subscription fee, but the software itself
has no support for monetary-based access restrictions, and there are
no plans to add that ability in the future.

Low
institutional costs

In addition to licensing,
institutions also face the "hidden" costs of hardware, software
support, and adapting existing practices. For organizations seeking
to publish their research in print, preparation costs can be immense.
Olorien tries to reduce all of these costs in a variety of ways:

Hardware
costs

The computer to run the Olorien
software and a constant Internet connection are one obvious
institutional cost. Olorien has been built to run on a variety of
operating systems, including Linux (free), FreeBSD (free), and Mac OS
X (not free).
One advantage to this approach is
that new, high-speed hardware is not needed. The processor-intensive
tasks of PDF and volume generation only happen once, then the results
are saved onto the hard drive. As a result, a used, older computer
running Linux makes a fine (and inexpensive) Olorien server.
Software Support Since Olorien is
open-source, it gains support from a community of users and
developers as the project gains popularity. As more institutions
deploy Olorien-based sites, similar snags in the setup and management
process will be documented, as well as the solutions to those
problems. The choice of open standards and common languages for the
construction of Olorien also aids in software support costs. If an
institution wishes to extend the Olorien architecture, they will have
little trouble finding skilled programmers.
Adapting existing practices
Olorien has been designed to mimic a traditional peer review process
as closely as possible. As a result, organization, which already has
a peer-reviewed publication, should find the transition painless.
Preparation for print for many
publications, the typesetting, organization, and preparation of
print-ready files is the most expensive and time-consuming part of
the publication process. Olorien greatly reduces these costs by
automatically preparing a PDF file that can be handed off to a press
for printing without changes.

Open
source

Olorien is open source software.
This means that the source code of Olorien is free for users to
download, use, and change. Olorien is released under the full GNU
Public License (GPL)[4]. In essence, the license says that the
software is released freely, with all source code for anyone to use
as they
please. The one stipulation is
that if anyone makes changes to the Olorien source, and
then uses the modified version in
a public context, they are required to release their
changes publicly, for no cost. We
have chosen the GPL as a license since innovation is likely to occur
on Olorien outside the bounds of Quantum Imagery, and it is in the
best interests of everyone in the scientific community if those
changes are shared. This means that Olorien is "free" in both
senses of the word. There is no cost to use the software, and its
source code can be modified without restriction, as long as those
changes are shared. In classic Internet terminology, Olorien is both
"free like speech" and "free like beer."

Figure 3: Olorien System Architecture

Technical
details

System
Architecture

Olorien is built using a variety
of widely available open-source technologies. It has been designed to
be as portable as possible across platforms and systems, and all of
the code used is platform independent. Olorien is made of three
primary parts: the database, the web application, and the supporting
article folders.
The Olorien database contains all
the content, review information, volume information, and user tables
for a journal. It does not contain any of the content for the actual
articles submitted, any attached images or figures, or the generated
PDFs. The web application is a set of PHP pages that link to several
external programs during PDF creation. The article folders house the
original submissions from the author, as well as all generated HTML,
PDF, and image files. This system is more efficient than keeping all
of the information in a single database because it lets each parent
system (the database and the file system) do the task it is good at.
Databases were not designed to manage large, binary files like PDFs,
and file systems were not designed for quick searching and retrieval
of small bits of data. It is also useful to note that on operating
systems where file access control is possible (Microsoft windows is
the notable exception), access to the files is exclusively limited to
the system user that runs the web server process. Since the data for
Olorien is split into two areas (the file system and the database),
it is important to make backups of both data stores. The Olorien
package comes with a sample shell script that should work well for
most backup needs. Interface Design Olorien is designed to be
lightweight, accessible, and easy to use.

Olorien uses Cascading Style
Sheets (CSS http://www.css.org) for its visual formatting and layout,
which allows users to quickly customize the look and feel of their
own journal to match their institutional needs. Since CSS is designed
to be backwards compatible, is completely accessible and usable in a
text-only environment.

Software
requirements to use Olorien

Olorien requires all of the
following packages to be installed on the server it runs on.

Note that several of the
platform-specific "QuickPackages" available on Quantum Imagery
already contain much of the above software pre-configured, and is a
good solution for most use needs.

How to use
it:

Complete step-by-step setup
instructions, QuickPackages, and user tutorials are available from
The Olorien web site http://www.quantumimagery.com/olorien. Questions
about setup and configuration can be sent to the author.

Future work
needed

Olorien is in active development,
and has a set of features planned to address current shortcomings.
Work is active on all of the following issues.
Limited Support for Article types
Olorien allows authors to upload plain text and HTML files, but more
direct conversions from popular programs are not possible at the
moment. In the future, Olorien should support:

At the moment, Olorien is only
supported on *nix-based operating systems, such as Mac OS X and
Linux. While this reaches the majority of the computers that act as
web servers, it may desirable to have support for other operating
systems, such as Microsoft's Windows TM. There is no code in
Olorien that prevents a quick and easy port to Windows, but at the
moment, that effort has not yet been undertaken. It is hoped that the
user community for Olorien will assist in porting the software to
other platforms Interface localization Though Olorien supports
localization of the entire site, the only language that is currently
translated is English. As users set up Olorien-based sites in their
own languages, we encourage them to send the translation files back
so that pre-built packages for various languages can be provided.
Multilingual support for full
body text Currently, users can specify an abstract and title in two
languages. However, this is not a complete solution for multilingual
publication. To truly meet this need, Olorien will support an
arbitrary number of languages for the title, abstract, and body text
of an article. Editors will be able to choose which language or set
of languages to publish for print, and all translations will be
available online.

Hosting
services

For institutions that do not want
to host their own copy of Olorien, a hosted version of Olorien will
also be offered in the future. This will allow subscribers to host
and manage their journal from a central server, without having to
manage the hardware and Internet connection. However, given the costs
of running a server, this service will probably not be free.

Conclusions

While several software frameworks
for journal management exist, none fully address the needs of NGOs
and institutions in developing countries. For these groups, Olorien
is an optimal solution. The management of journal creation from
submission all the way through archiving allows these organizations
to have a quality, peer-reviewed journal that might otherwise not be
affordable. Low publication costs allow institutions to publish more
research, allowing an increase in research funding, and turning the
'downward spiral' that can characterize low-budget organizations
around. While obviously geared toward NGOs and developing
institutions, Olorien is a complete solution for established research
organizations looking to move to a more automated system with a
web-based presence. It is feature complete, and undergoing active
development for future improvements. Over the next year, Olorien will
add support for Windows servers, more document upload formats, and
interface localization. The community of organizations deploying
Olorien will help accelerate this process.